The long-term objectives of this application are to identify microorganisms as well as human cellular pathways that promote Crohn?s disease, and to develop novel diagnostic tools and therapeutic strategies for this disease. The short-term objectives include the identification of microflora and host expression patterns that are associated with disease activity, and assessment of molecular methods for pathogen identification. The specific aims are: Aim 1: Identify bacterial and archaeal species associated with active Crohn?s disease using broad range ribosomal DNA PCR, laser capture microdissection, and fluorescent in situ hybridization. Tissues with ulcerative colitis, inactive Crohn?s disease, and no apparent disease will serve as some of the controls. Aim 2: Quantify differences in relative abundance of bacterial and archaeal species found in Crohn?s disease and controls. An rDNA microarray will be used, as well as a more traditional slot-blot hybridization approach. Aim 3: Identify global host gene expression patterns in intestinal tissue and peripheral blood that are associated with Crohn?s disease. Expression patterns will be defined that correlate with disease state and activity, and with bacterial and archaeal microflora profiles. State of the art, high-density human cDNA microarrays, and both unsupervised and supervised pattern recognition algorithms will be used to reveal disease-associated signatures. This combination of approaches offers opportunities for characterizing Crohn?s disease, and for examining the complex interactions of human host and microbial flora during states of health and disease.